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- EMDB-4086: RNA polymerase I-Rrn3 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-4086
TitleRNA polymerase I-Rrn3 complex
Map data
SampleS. cerevisiae RNA polymerase I in complex with activating factor Rrn3
Biological speciesSaccharomyces cerevisiae (baker's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.7 Å
AuthorsTorreira E / Louro JA / Gil-Carton D / Gallego O / Calvo O / Fernandez-Tornero C
CitationJournal: Elife / Year: 2017
Title: The dynamic assembly of distinct RNA polymerase I complexes modulates rDNA transcription.
Authors: Eva Torreira / Jaime Alegrio Louro / Irene Pazos / Noelia González-Polo / David Gil-Carton / Ana Garcia Duran / Sébastien Tosi / Oriol Gallego / Olga Calvo / Carlos Fernández-Tornero /
Abstract: Cell growth requires synthesis of ribosomal RNA by RNA polymerase I (Pol I). Binding of initiation factor Rrn3 activates Pol I, fostering recruitment to ribosomal DNA promoters. This fundamental ...Cell growth requires synthesis of ribosomal RNA by RNA polymerase I (Pol I). Binding of initiation factor Rrn3 activates Pol I, fostering recruitment to ribosomal DNA promoters. This fundamental process must be precisely regulated to satisfy cell needs at any time. We present in vivo evidence that, when growth is arrested by nutrient deprivation, cells induce rapid clearance of Pol I-Rrn3 complexes, followed by the assembly of inactive Pol I homodimers. This dual repressive mechanism reverts upon nutrient addition, thus restoring cell growth. Moreover, Pol I dimers also form after inhibition of either ribosome biogenesis or protein synthesis. Our mutational analysis, based on the electron cryomicroscopy structures of monomeric Pol I alone and in complex with Rrn3, underscores the central role of subunits A43 and A14 in the regulation of differential Pol I complexes assembly and subsequent promoter association.
History
DepositionAug 2, 2016-
Header (metadata) releaseAug 10, 2016-
Map releaseMar 22, 2017-
UpdateJul 12, 2017-
Current statusJul 12, 2017Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.11
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.11
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_4086.map.gz / Format: CCP4 / Size: 16.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.77 Å/pix.
x 162 pix.
= 286.74 Å
1.77 Å/pix.
x 162 pix.
= 286.74 Å
1.77 Å/pix.
x 162 pix.
= 286.74 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.77 Å
Density
Contour LevelBy AUTHOR: 0.11 / Movie #1: 0.11
Minimum - Maximum-0.09232628 - 0.28997466
Average (Standard dev.)0.00456031 (±0.023206301)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions162162162
Spacing162162162
CellA=B=C: 286.74 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.771.771.77
M x/y/z162162162
origin x/y/z0.0000.0000.000
length x/y/z286.740286.740286.740
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS162162162
D min/max/mean-0.0920.2900.005

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Supplemental data

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Sample components

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Entire S. cerevisiae RNA polymerase I in complex with activating factor Rrn3

EntireName: S. cerevisiae RNA polymerase I in complex with activating factor Rrn3
Number of components: 1

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Component #1: protein, S. cerevisiae RNA polymerase I in complex with activatin...

ProteinName: S. cerevisiae RNA polymerase I in complex with activating factor Rrn3
Recombinant expression: No
MassTheoretical: 594 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.06 mg/mL / pH: 7.8
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 95 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 68 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 47000.0 X (nominal), 79096.0 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1900.0 - 4200.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON II (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 1288

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 32175
3D reconstructionSoftware: RELION / Resolution: 7.7 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Refinement protocol: rigid body / Refinement space: REAL / Overall bvalue: 537

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